Criteria Specification Registry

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ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.2

Description: TP53 Rule Specifications for the ACMG/AMP Variant Curation Guidelines

Expert Panel: TP53 VCEP

Approval Status: Approved - Step 4

Last Updated: 08-06-2019

Version: 1.2.0

Release Notes:
• Corrected formatting and typos.
• Provided clarifying language to facilitate understanding and application of rule specifications (April 2021).

PDF Document:

JSON-LD Document:

Rules for TP53

Gene: TP53 (HGNC:11998) HGNC Name: tumor protein p53 Preferred Transcript: NM_000546.4 Disease: Li-Fraumeni syndrome (MONDO:0018875)

Criteria	Original ACMG Summary	Strength Specifications
PVS1	Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease. Caveats: • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7). • Use caution interpreting LOF variants at the extreme 3’ end of a gene. • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact. • Use caution in the presence of multiple transcripts.	Very Strong Defer to SVI recommendations
PS1	Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Example: Val->Leu caused by either G>C or G>T in the same codon. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.	Strong Must confirm there is no difference in splicing using RNA data. Can only compare to variants asserted as pathogenic by the ClinGen TP53 EP. Moderate Must confirm there is no difference in splicing using in silico modeling data using a splice metapredictor (SpliceAI, VarSEAK, etc). Can only compare to variants asserted as pathogenic by the ClinGen TP53 EP.
PS2	De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity.	Very Strong Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. ≥4 points (ex. – 2 cancers in two probands from the strong criteria list or 4 cancers from 4 probands from the moderate criteria). For probands with multiple cancers, use the most specific/highest weight cancer to determine point for that proband. Strong Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 2-3 points (ex. – 1 cancer from the strong criteria list or 2 from the moderate criteria list) Moderate Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 1 point (for 1 cancer from the moderate criteria list) Supporting Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 0.5 point (1 cancer from the moderate criteria list)
PS3	Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.	Strong Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a low functioning allele (<= 20% activity) AND: • Evidence of dominant negative effect (DNE) + evidence of LOF from Giacomelli, et al data OR • There is a 2nd assay showing low function (colony formation assays, apoptosis assays, tetramer assays, knock-in mouse models and growth suppression assays) Do not use code with conflicting evidence Moderate (A) Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a partially functioning allele (>20-and <=75% activity) AND: • Evidence of DNE + evidence of LOF from Giacomelli, et al data. OR • There is a 2nd assay showing low function. Do not use code with conflicting evidence. (B) No transactivation assays (IARC classification based on data Kato et al, 2003) available BUT: • Evidence of DNE + evidence of LOF from Giacomelli, et al data. AND • There is a 2nd assay showing low function Do not use code with conflicting evidence.
PS4	The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.	Strong Use proband counting system described below in text. PS4 = 4+ points Moderate Use proband counting point system described in text below. PS4_moderate = 2-3 points Supporting Use proband counting point system described in text below. PS4_Suppporting = 1 point
PM1	Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.	Moderate This rule can be applied to variants in hot spots (codons 175, 245, 248, 249, 273, 282), but not to variants within functional domains. Use transcript NM_000546.4. Also use rule for variants with ≥10 somatic observations cancerhotspots.org (v2)
PM2	Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Caveat: Population data for indels may be poorly called by next generation sequencing.	Supporting Variant needs to be absent from controls. The variant must be absent from population databases. gnomAD is the preferred population database at this time (http://gnomad.broadinstitute.org). The most recent version of gnomAD with a non-cancer subpopulation should be used; however, other versions may be utilized if there is reason to believe they would provide necessary information for curating the variant.
PM3	For recessive disorders, detected in trans with a pathogenic variant Note: This requires testing of parents (or offspring) to determine phase.	Not Applicable This rule does not apply to TP53/Li_Fraumeni syndrome.
PM4	Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.	Not Applicable This rule should not be used at this time due to limited data.
PM5	Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. Example: Arg156His is pathogenic; now you observe Arg156Cys. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.	Moderate Multiple pathogenic variants (≥2) at that residue using the requirements specified below (excluding known hot spots) would be required. Grantham should be used to compare the variants. At least one of the new variants must be equal or worse than known pathogenic variant. Splicing should be ruled out. Can only compare to variants asserted as pathogenic by the ClinGen TP53 EP. Rule cannot be used in conjunction with PM1. Supporting Grantham should be used to compare variants. The new variant must be equal or worse than known mutation. Splicing should be ruled out. Rule cannot be used in conjunction with PM1.
PM6	Assumed de novo, but without confirmation of paternity and maternity.	Very Strong Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. ≥4 points (ex. – 2 cancers in two probands from the strong criteria list or 4 cancers from 4 probands from the moderate criteria). For probands with multiple cancers, use the most specific/highest weight cancer to determine point for that proband. Strong Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 2-3 points (ex. – 1 cancer from the strong criteria list or 2 from the moderate criteria list) Moderate Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 1 point (for 1 cancer from the moderate criteria list) Supporting Use SVI point system table. See Cancer Criteria List & TP53 Point Table at end of document. 0.5 point (1 cancer from the moderate criteria list)
PP1	Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Note: May be used as stronger evidence with increasing segregation data.	Strong Cosegregation must be observed ≥7 meioses in >1 family in to apply this rule. Moderate Cosegregation must be observed in 5-6 meioses in 1 family to apply this rule. Supporting Cosegregation must be observed in 3-4 meioses in 1 family to apply this rule
PP2	Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.	Not Applicable This rule does not apply due to the high number of benign missense variation.
PP3	Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant.	Moderate PolyPhen2 and SIFT in silico modeling programs should not be used for this gene. Missense variants: aGVGD (Zebrafish; Class C65 required) and BayesDel (score ≥ 0.16) Supporting PolyPhen2 and SIFT in silico modeling programs should not be used for this gene. Concordance of two predictors is recommended for this gene: • Missense variants: aGVGD (Zebrafish; Class C25 and higher are considered evidence of pathogenicity) and BayesDel (scores ≥ 0.16 are considered evidence of pathogenic) • Splicing variants: Evidence of splice effect on a splice metapredictor (SpliceAI, VarSEAK, etc).
PP4	Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.	Supporting Use modified PS4 criteria instead of PP4 code
PP5	Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.	Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BA1	Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.	Stand Alone Frequency cutoff of 0.1% minimum of 5 alleles present in the population
BS1	Allele frequency is greater than expected for disorder.	Strong Frequency cutoff of 0.03%; minimum of 5 alleles present in the population. • Use a minor allele frequency cutoff of >0.0003 but <0.001 (99.99% CI, sub-population must have a minimum of 5 alleles present in the sub-population) based on the Whiffen-Ware calculator. • To set the strong benign MAF cutoff, we used a prevalence of 1 in 5,000 from Lalloo, et a 2006 (PMID:16644204). We set the genetic and allelic heterogeneity at 100% and penetrance at 30%.
BS2	Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.	Strong Observed in ≥8 cancer free 60+ year old females obtained from the same data source. Using TP53 multigene panel testing results from two diagnostic labs, we compared the proportion of cancer-free individuals by age 60 in TP53 carriers versus TP53-negative controls. Based on the correspondence between likelihood ratios of pathogenicity and different levels of strengths for ACMG/AMP rules in the study by Tavtigian et al., 2018 (PMID: 29300386), our most conservative results support the following: • This evidence code can be used when a variant is observed in ≥8 females who have reached at least 60 years of age without cancer. These individuals all must have come from a single source (single lab, database, etc). Cases cannot be counted across sources. Supporting Observed in 2-7 cancer free 60+ year old females obtained from the same data source. Using TP53 multigene panel testing results from two diagnostic labs, we compared the proportion of cancer-free individuals by age 60 in TP53 carriers versus TP53-negative controls. Based on the correspondence between likelihood ratios of pathogenicity and different levels of strengths for ACMG/AMP rules in the study by Tavtigian et al., 2018 (PMID: 29300386), our most conservative results support the following: • This evidence code can be used when a variant is observed in 2-7 females who have reached at least 60 years of age without cancer. These individuals all must have come from a single source (single lab, database, etc). Cases cannot be counted across sources.
BS3	Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.	Strong Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that show retained function (76-140% activity) or supertransactivation function AND: • No evidence of DNE + no evidence of LOF from Giacomelli, et al data. OR There is a 2nd assay, including colony formation assays, apoptosis assays, tetramer assays, growth suppression and knock-in mouse models demonstrating retained function. Do not use code with conflicting evidence Supporting Transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) that demonstrate a partially functioning allele (>20% and <=75% activity) AND: • No evidence of DNE + no evidence of LOF from Giacomelli, et al data. OR • There is a 2nd assay demonstrating retained function Do not use code with conflicting evidence. No transactivation assays in yeast (IARC classification based on data from Kato et al, 2003) available BUT: • No evidence of DNE + no evidence of LOF from Giacomelli, et al data. AND There is a 2nd assay showing retained function Do not use code with conflicting evidence
BS4	Lack of segregation in affected members of a family. Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation.	Strong Variant segregates to opposite side of the family who meets LFS criteria. OR Variant is present in ≥3 living unaffected individuals (at least 2 of which should be female) above 55 years of age.
BP1	Missense variant in a gene for which primarily truncating variants are known to cause disease.	Not Applicable This rule code does not apply to these genes, as truncating variants account for only a portion of disease causing variants.
BP2	Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.	Supporting This evidence code can be applied in either scenario below: • Variant is observed in trans with a pathogenic or likely pathogenic TP53 variant (phase confirmed), or • When there are 3 or more observations with a pathogenic or likely pathogenic variant when phase is unknown. In this scenario, the variant must be seen with at least two different pathogenic/likely pathogenic TP53 variants.
BP3	In frame-deletions/insertions in a repetitive region without a known function.	Not Applicable Do not use this rule at this time.
BP4	Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant.	Supporting Missense: aGVGD (zebrafish; Class C0 or C15 is considered evidence of non-pathogenicity) and BayesDel <0.16 is considered evidence on non-pathogenicity Splicing: Evidence of splice effect on a splice metapredictor (SpliceAI, VarSEAK, etc).
BP5	Variant found in a case with an alternate molecular basis for disease.	Not Applicable This rule code is not recommended for use at this time.
BP6	Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.	Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BP7	A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.	Supporting Evidence of splice effect on a splice metapredictor (SpliceAI, VarSEAK, etc). If a new alternate site is predicted, compare strength to native site in interpretation.